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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAATGTCATTGAAGAGATTATGATTGGGGAGGACAAACTTATTCACTTCTCTGGTGTCGCGATGGGCCAGGCTTGCACCATTGTTTTAAGAGGAGCAAGgtatgccttttttgttcacacgcatccttgtgtagcataattttgtaattttcatatgtttttatacgtactatatttatgtgtttttgttttctacag

Basic information

species Oryza sativa
transcript LOC_Os03g42220.2
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g42220.1 (Oryza sativa), 5'ss of exon 9
lower sequence: EF517601.1_FGT012 (Zea mays), 5'ss of exon 17
GCAATGTCATTGAAGAGATTATGATTGGGGAGGACAAACTTATTCACTTCTCTGGTGTCGCGATGGGCCAGGCTTGCACCATTGTTTTAAGAGGAGCAAGgtatgccttttttgttcacacgcatccttgtgtagcataattttgtaattttcatatgt---ttttatacgtactatatttatgtgtttttgt-tttctacag
|||| |||||||||||||||||||||||||||||||  || || || |||||||| || |||||||| |||||||||||||||||  |||| || || ||||||| | | ||| ||   ||  ||| || |    |  |||| |   || |    || |   ||||  |   | |   | | | || ||||   |  || |||
GCAAGGTCATTGAAGAGATTATGATTGGGGAGGACAGGCTAATCCATTTCTCTGGGGTTGCGATGGGGCAGGCTTGCACCATTGTCCTAAGGGGGGCTAGgtatgtcatgttttttactacttatcatt-taggactaaattgttccatctatgcatttcaattttccataaattgagtctttttgctttttcatccctgcag

upper sequence: LOC_Os03g42220.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G058276_T01 (Zea mays), 5'ss of exon 8
GCAATGTCATTGAAGAGATTATGATTGGGGAGGACAAACTTATTCACTTCTCTGGTGTCGCGATGGGCCAGGCTTGCACCATTGTTTTAAGAGGAGCAAGgtatgccttttttgttcacacgcatcc-ttgtgtagcataattttgtaattttcatatgtttttatacgtactatatttatgtgtttttgttttctacag---------
|||| || ||||||||||| ||||||||||||||||   | ||||| |||||||| ||||||||||| ||||||||||||||||| ||||| || || ||||||| ||| ||  | |||    |    |  || || |  | | |||    |  ||   |||  | |  | |   | ||  || |||||| ||| |             
GCAAGGTAATTGAAGAGATCATGATTGGGGAGGACAGGTTAATTCATTTCTCTGGGGTCGCGATGGGGCAGGCTTGCACCATTGTCTTAAGGGGGGCTAGgtatgtcttgttc-tacacttctacttatcatgcaggactactatgttccatctatgcatttcaa-atttccataaattgagtatttttgctttttttcatccctgcag

upper sequence: LOC_Os03g42220.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA12G09250.1 (Glycine max), 5'ss of exon 10
GCAATGTCATTGAAGAGATTATGATTGGGGAGGACAAACTTATTCACTTCTCTGGTGTCGCGATGGGCCAGGCTTGCACCATTGTTTTAAGAGGAGCAAGgtatgc----cttttttgttcacacgcatccttgtgtagcataattttgta-attttcatatgtttttatacgtactatatt-tatgtgtttttgttttctacag
|| |  | ||||| |||||||||||||| ||||| ||||| ||||| || |||||||| || ||||| ||||| || || || ||||| ||||| || |||||       || |||| ||       | || | |  ||  |  ||||  | | |     || || || |   ||  ||||| |||    | || || ||     
GCGACCTTATTGAGGAGATTATGATTGGCGAGGATAAACTGATTCATTTTTCTGGTGTTGCTATGGGGCAGGCATGTACAATAGTTTTGAGAGGTGCTAGgtacttgttgctcttttattatttaaaacccctttcaagtgttcttttacatagtcaggcattttattgttgataacatattatatcaaatctttttgtc-----

upper sequence: LOC_Os03g42220.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA11G19220.1 (Glycine max), 5'ss of exon 10
GCAATGTCATTGAAGAGATTATGATTGGGGAGGACAAACTTATTCACTTCTCTGGTGTCGCGATGGGCCAGGCTTGCACCATTGTTTTAAGAGGAGCAAGgtatgccttttttgttcac-acgcatccttgtgtagcataattttgtaattttcatatgtttttatacgtactatatt-tatgtgtttttgttttctacag
|  |  | ||||| |||||||||||||| ||||| ||||| ||||| || |||||||| || ||||| ||||| || || || ||| | ||||| || |||||    ||  |  || |  |   |        |  ||   ||     | ||    || || || |   ||  |||||   |    | || ||||   || 
GTGACCTTATTGAGGAGATTATGATTGGCGAGGATAAACTGATTCATTTTTCTGGTGTTGCTATGGGGCAGGCATGTACAATAGTTCTGAGAGGGGCTAGgtacttgttactcatttattatttaaaacccctttccagtgttcgtatacttaggcattttattgttaataacatattacgtcaaatcttttttttgtca-

upper sequence: LOC_Os03g42220.1 (Oryza sativa), 5'ss of exon 9
lower sequence: PP1S116_55V6.1 (Physcomitrella patens), 5'ss of exon 9
GCAATGTCATTGAAGAGATTATGATTGGGGAGGACAAACTTATTCACTTCTCTGGTGTCGCGATGGGCCAGGCTTGCACCATTGTTTTAAGAGGAGCAAGgtatgccttttttgttcacacgcatccttgtgtagcataattttgtaattttcatatgtttttata-cgtactatatttatgtgtt-tttgttttctacag--------------------------------------------------------------------------------
| ||  | ||||||||||| |||||||| || ||||||||||| || || || ||||| || ||||| | |||||| ||||||||  || | || || ||||  ||   |   |      | ||| | | | |    |  | ||||| ||   |      | | |  | ||||     | | |  | |||||||| |  |                                                                                 
GTAAATTAATTGAAGAGATCATGATTGGTGAAGACAAACTTATCCATTTTTCAGGTGTTGCAATGGGGCGGGCTTGTACCATTGTCCTACGTGGTGCCAGgttagcacctcccgcatggtctcattcatttat----tggtattgtatttcgtaaggaagtatgtgtcttacttggcctttattctatttgttttatgtaaataatcctttcactattttgaacttgtgtttgaaatccgatcatgacaatcttctttgttatgtggtgttcctttggcag

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|29676854|gb|CB673129.1|CB673129
EST:     TCTGGTGTCGCGATGGGCCAGGCTTGCACCATTGTTTTAAGAGGAGCAAG                         TGAGCATGTGCTTGACGAGGCTGAGAGGTCCTTGCACGATGCCTTATGTGT
genomic: TCTGGTGTCGCGATGGGCCAGGCTTGCACCATTGTTTTAAGAGGAGCAAGgtatgccttt ... ttttctacagTGAGCATGTGCTTGACGAGGCTGAGAGGTCCTTGCACGATGCCTTATGTGT
EST: gi|38481744|gb|CF965819.1|CF965819
EST:     TCTGGTGTCGCGATGGGCCAGGCTTGCACCATTGTTTTAAGAGGAGCAAG                         TGAGCATGTGCTTGACGAGGCTGAGAGGTCCTTGCACGATGCCTTATGTGT
genomic: TCTGGTGTCGCGATGGGCCAGGCTTGCACCATTGTTTTAAGAGGAGCAAGgtatgccttt ... ttttctacagTGAGCATGTGCTTGACGAGGCTGAGAGGTCCTTGCACGATGCCTTATGTGT
EST: gi|218499498|gb|FG967620.1|FG967620
EST:     TCTGGTGTCGCGATGGGCCAGGCTTGCACCATTGTTTTAAGAGGAGCAAG                         TGAGCATGTGCTTGACGAGGCTGAGAGGTCCTTGCACGATGCCTTATGTGT
genomic: TCTGGTGTCGCGATGGGCCAGGCTTGCACCATTGTTTTAAGAGGAGCAAGgtatgccttt ... ttttctacagTGAGCATGTGCTTGACGAGGCTGAGAGGTCCTTGCACGATGCCTTATGTGT
EST: gi|29657047|gb|CB653322.1|CB653322
EST:     CGCGATGGGCCAGGCTTGCACCATTGTTTTAAGAGGAGCAAG                         TGAGCATGTGCTTGACGAGGCTGAGAGGTCCTTGCACGATGCCTTATGTGT
genomic: CGCGATGGGCCAGGCTTGCACCATTGTTTTAAGAGGAGCAAGgtatgccttt ... ttttctacagTGAGCATGTGCTTGACGAGGCTGAGAGGTCCTTGCACGATGCCTTATGTGT
EST: gi|38476603|gb|CF960736.1|CF960736
EST:     TCTGGTGTCGCGATGGGCCAGGCTTGCACCATTGTTTTAAGAGGAGCAAG                         TGAGCATGTGCTTGACGAGGCTGAGAGGTCCTTGCACGATGCCTTATGTGT
genomic: TCTGGTGTCGCGATGGGCCAGGCTTGCACCATTGTTTTAAGAGGAGCAAGgtatgccttt ... ttttctacagTGAGCATGTGCTTGACGAGGCTGAGAGGTCCTTGCACGATGCCTTATGTGT
EST: gi|218484326|gb|FG955561.1|FG955561
EST:     TCTGGTGTCGCGATGGGCCAGGCTTGCACCATTGTTTTAAGAGGAGCAAG                         TGAGCATGTGCTTGACGAGGCTGAGAGGTCCTTGCACGATGCCTTATGTGT
genomic: TCTGGTGTCGCGATGGGCCAGGCTTGCACCATTGTTTTAAGAGGAGCAAGgtatgccttt ... ttttctacagTGAGCATGTGCTTGACGAGGCTGAGAGGTCCTTGCACGATGCCTTATGTGT
EST: gi|29616346|gb|CB621358.1|CB621358
EST:     TCTGGTGTCGCGATGGGCCAGGCTTGCACCATTGTTTTAAGAGGAGCAAG                         TGAGCATGTGCTTGACGAGGCTGAGAGGTCCTTGCACGATGCCTTATGTGT
genomic: TCTGGTGTCGCGATGGGCCAGGCTTGCACCATTGTTTTAAGAGGAGCAAGgtatgccttt ... ttttctacagTGAGCATGTGCTTGACGAGGCTGAGAGGTCCTTGCACGATGCCTTATGTGT
EST: gi|58686292|gb|CK074979.1|CK074979
EST:     TCTGGTGTCGCGATGGGCCAGGCTTGCACCATTGTTTTAAGAGGAGCAAG                         TGAGCATGTGCTTGACGAGGCTGAGAGGTCCTTGCACGATGCCTTATGTGT
genomic: TCTGGTGTCGCGATGGGCCAGGCTTGCACCATTGTTTTAAGAGGAGCAAGgtatgccttt ... ttttctacagTGAGCATGTGCTTGACGAGGCTGAGAGGTCCTTGCACGATGCCTTATGTGT
EST: gi|86823862|gb|CI258850.1|CI258850
EST:     TCTGGTGTCGCGATGGGCCAGGCTTGCACCATTGTTTTAAGAGGAGCAAG                         TGAGCATGTGCTTGACGAGCCTGAGAGGTCCTTGCACGATGCCTTATGTGT
genomic: TCTGGTGTCGCGATGGGCCAGGCTTGCACCATTGTTTTAAGAGGAGCAAGgtatgccttt ... ttttctacagTGAGCATGTGCTTGACGAGGCTGAGAGGTCCTTGCACGATGCCTTATGTGT
EST: gi|27554034|gb|CA997934.1|CA997934
EST:     TCTGGTGTCGCGATGGGCCAGGCTTGCACCATTGTTTTAAGACGAGCAAG                         TGAGCATGTGCTTGACGAGGCTGAGAGGTTCTTGCACGATGCCTTATG
genomic: TCTGGTGTCGCGATGGGCCAGGCTTGCACCATTGTTTTAAGAGGAGCAAGgtatgccttt ... ttttctacagTGAGCATGTGCTTGACGAGGCTGAGAGGTCCTTGCACGATGCCTTATG
EST: gi|58679038|gb|CK067725.1|CK067725
EST:     TCTGGTGTCGCGATGGGCCAGGCTTGCACCATTGTTTTAAGAGGAGCAAG                         TGAGCATGTGCTTGACGAGGCTGAGAGGTCCTTGCACGATGCCTTATGTGT
genomic: TCTGGTGTCGCGATGGGCCAGGCTTGCACCATTGTTTTAAGAGGAGCAAGgtatgccttt ... ttttctacagTGAGCATGTGCTTGACGAGGCTGAGAGGTCCTTGCACGATGCCTTATGTGT
EST: gi|58681953|gb|CK070640.1|CK070640
EST:     TCTGGTGTCGCGATGGGCCAGGCTTGCACCATTGTTTTAAGAGGAGCAAG                         TGAGCATGTGCTTGACG
genomic: TCTGGTGTCGCGATGGGCCAGGCTTGCACCATTGTTTTAAGAGGAGCAAGgtatgccttt ... ttttctacagTGAGCATGTGCTTGACG
EST: gi|58653416|gb|CK042096.1|CK042096
EST:     TCTGGTGTCGCGATGGGCCAGGCTTGCACCATTGTTTTAAGAGGAGCAAG                         TGAGCATGTGCTTGACGAGGCTGAGAGGTCCTTGCACGATGCCTTATGTGT
genomic: TCTGGTGTCGCGATGGGCCAGGCTTGCACCATTGTTTTAAGAGGAGCAAGgtatgccttt ... ttttctacagTGAGCATGTGCTTGACGAGGCTGAGAGGTCCTTGCACGATGCCTTATGTGT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 73 (upstream exon), 70 (downstream exon)
Score: 23

GCAATGTCATTGAAGAGATTATGATTGGGGAGGACAAACTTATTCACTTCTCTGGTGTCGCGATGGGCCAGGCTTGCACCATTGTTTTAAGAGGAGCAAGgtatgccttt ... ttttctacagTGAGCATGTGCTTGACGAGGCTGAGAGGTCCTTGCACGATGCCTTATGTGTGCTTTCCCAGACAGTAAATGACACCCGTGTCTTATTTGGGGGTGGTTGG




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Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCAATGTCATTGAAGAGATTATGATTGGGGAGGACAAACTTATTCACTTCTCTGGTGTCGCGATGGGCCAGGCTTGCACCATTGTTTTAAGAGGAGCAAGgtatgccttttttgttcacacgcatccttgtgtagcataattttgtaattttcatatgtttttatacgtactatatttatgtgtttttgttttctacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG